The quarterback controversy by the bay looks like it will continue to drag on for the remainder of the 2012 NFL season, but it increasingly looks like second-year signal-caller Colin Kaepernick has the inside track on the job. On Wednesday, 49ers head coach Jim Harbaugh named Kaepernick the starter for San Francisco’s Sunday matchup with the St. Louis Rams.

While Harbaugh hasn’t named Kaepernick his starter for the rest of the season, it’s clear that the Nevada product allows the 49ers to do more on offense than incumbent starter Alex Smith.

Before being relegated to backup status, Smith had completed 70 percent of his passes and had a career-high quarterback rating of 104.1 through nine games. Smith had also racked up 1,731 yards through the air, with 13 touchdowns and just five interceptions. That’s not a bad stat line, and the 49ers looked like one of the NFL’s best teams. So when was the last time a guy with numbers like that actually lost his job?

So far this season, Kaepernick has completed 64.9 percent of his passes and has a quarterback rating of 102.3. The 49ers have won both games with Kaepernick starting under center and Harbaugh has claimed he will go with the “hot hand,” which is currently Kaepernick.

Harbaugh explained his position on Wednesday, saying the following:

“The rationale is we have two quarterbacks that we feel great about as a starting quarterback. Both have earned it, both deserve it – Alex over a long period of time, Colin by virtue of the last three games. It tips the scales. Colin we believe has the hot hand. We’ll go with Colin. And we’ll go with Alex. They’re both our guys.”

Smith was forced from the 49ers game against the Rams on November 11 when he suffered a concussion. Kaepernick relieved him and hasn’t relinquished the job since. During San Francisco’s 31-21 win over the New Orleans Saints on Sunday, Smith hardly looked happy on the sidelines as Kaepernick did his thing as the starter.

You have to feel bad for Smith here. Since he was taken with the No. 1 overall pick in the 2005 NFL Draft, his position in San Francisco has never been stable. Imagine having to fight for your job every week for eight seasons. That would leave anyone a little salty.

But the writing is on the wall in San Francisco. Kaepernick is the team’s future at quarterback, so don’t be surprised if Smith doesn’t get his job back this season. Unless Kaepernick gets injured it’s safe to say he will be the starter in San Francisco for quite some time.